|
| Status |
Public on Feb 01, 2016 |
| Title |
38-1 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Immediately before surgery
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Muscle biopsy immediately before surgery
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lexogen QuantSeq mRNA-seq kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequencing and basecalling by Illumina HiSeq Control Software 2.2.58
BCL conversion and demultiplexing by Illumina CASAVA 1.8.2
FASTQ files aligned to Homo_sapiens.GRCh38.dna.toplevel.fa genome assembly obtained from ENSEMBL. The Homo_sapiens.GRCh38.78.gtf file from ENSEMBL was used for annotation. Alignments were performed with STAR 2.4.0i.
Gene count tables were generated from STAR-produced SAM files using HTSeq-count 0.6.1
genome build: Homo_sapiens.GRCh38.dna.toplevel.fa
.counts files: Gene count tables generated by HTSeq-count from each .sam file for each sample
|
| |
|
| Submission date |
Nov 27, 2015 |
| Last update date |
Aug 30, 2022 |
| Contact name |
Hans Christian Dreyer |
| E-mail(s) |
hcdreyer@uoregon.edu
|
| Organization name |
University of Oregon
|
| Department |
Human Physiology
|
| Lab |
Muscle Physiology
|
| Street address |
1240 University of Oregon
|
| City |
Eugene |
| State/province |
Oregon |
| ZIP/Postal code |
97403-1240 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE75432 |
Muscle transcriptome analysis following Total Knee Arthroplasty with Tourniquet |
|
| Relations |
| BioSample |
SAMN04297340 |
| SRA |
SRX1453165 |
